Starting phenix.real_space_refine on Thu Aug 8 20:04:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yeo_39200/08_2024/8yeo_39200.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yeo_39200/08_2024/8yeo_39200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yeo_39200/08_2024/8yeo_39200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yeo_39200/08_2024/8yeo_39200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yeo_39200/08_2024/8yeo_39200.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yeo_39200/08_2024/8yeo_39200.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 120 5.16 5 C 15024 2.51 5 N 4065 2.21 5 O 4870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24197 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2010 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "J" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2718 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 322} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2639 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 12, 'rna3p_pur': 21, 'rna3p_pyr': 10} Link IDs: {'rna2p': 27, 'rna3p': 32} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2412 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "E" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2621 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "F" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "G" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "H" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "N" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 13.15, per 1000 atoms: 0.54 Number of scatterers: 24197 At special positions: 0 Unit cell: (136.85, 145.35, 164.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 118 15.00 O 4870 8.00 N 4065 7.00 C 15024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.09 Conformation dependent library (CDL) restraints added in 4.3 seconds 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5106 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 38 sheets defined 33.8% alpha, 19.4% beta 40 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 8.95 Creating SS restraints... Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.824A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.563A pdb=" N CYS A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'J' and resid 2 through 9 Processing helix chain 'J' and resid 15 through 31 removed outlier: 3.882A pdb=" N TYR J 23 " --> pdb=" O LYS J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 86 Processing helix chain 'J' and resid 87 through 93 Processing helix chain 'J' and resid 111 through 121 removed outlier: 3.861A pdb=" N GLU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 134 removed outlier: 3.651A pdb=" N ASN J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 179 Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 201 through 206 Processing helix chain 'J' and resid 217 through 221 removed outlier: 3.709A pdb=" N GLU J 221 " --> pdb=" O LYS J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 230 removed outlier: 3.533A pdb=" N ALA J 227 " --> pdb=" O ASN J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 242 removed outlier: 3.530A pdb=" N GLU J 241 " --> pdb=" O ASN J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 267 removed outlier: 4.311A pdb=" N LEU J 258 " --> pdb=" O ALA J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 293 removed outlier: 3.644A pdb=" N PHE J 288 " --> pdb=" O THR J 284 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU J 289 " --> pdb=" O VAL J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 312 Processing helix chain 'J' and resid 316 through 318 No H-bonds generated for 'chain 'J' and resid 316 through 318' Processing helix chain 'J' and resid 326 through 340 Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.534A pdb=" N ASP B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.553A pdb=" N CYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 removed outlier: 4.358A pdb=" N ARG B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 removed outlier: 4.196A pdb=" N LYS B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 70 Processing helix chain 'I' and resid 102 through 104 No H-bonds generated for 'chain 'I' and resid 102 through 104' Processing helix chain 'I' and resid 112 through 129 Processing helix chain 'I' and resid 131 through 144 Processing helix chain 'I' and resid 145 through 152 removed outlier: 6.178A pdb=" N ARG I 150 " --> pdb=" O PHE I 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG I 152 " --> pdb=" O TRP I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 202 removed outlier: 3.625A pdb=" N GLN I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 259 removed outlier: 3.594A pdb=" N ALA I 257 " --> pdb=" O LYS I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.649A pdb=" N TYR I 271 " --> pdb=" O ASP I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 306 Processing helix chain 'I' and resid 312 through 326 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.536A pdb=" N LEU D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.644A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.877A pdb=" N GLU E 68 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 removed outlier: 4.412A pdb=" N MET E 106 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.675A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.512A pdb=" N LEU E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP E 149 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 153 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 186 through 201 removed outlier: 3.721A pdb=" N GLN E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.562A pdb=" N ILE E 254 " --> pdb=" O HIS E 250 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 3.812A pdb=" N TYR E 271 " --> pdb=" O ASP E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.766A pdb=" N LEU E 323 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 324 " --> pdb=" O MET E 320 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 70 Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.688A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.644A pdb=" N TRP F 149 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.677A pdb=" N GLN F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.651A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 112 through 129 removed outlier: 3.596A pdb=" N TYR G 119 " --> pdb=" O ARG G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 145 through 153 removed outlier: 3.506A pdb=" N LEU G 148 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP G 149 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS G 153 " --> pdb=" O ARG G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.654A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.735A pdb=" N ALA G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 removed outlier: 3.526A pdb=" N ILE G 305 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 removed outlier: 4.033A pdb=" N LEU G 323 " --> pdb=" O VAL G 319 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G 324 " --> pdb=" O MET G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.914A pdb=" N ARG H 40 " --> pdb=" O PHE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.555A pdb=" N ARG H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.526A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.618A pdb=" N LEU H 148 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.577A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.644A pdb=" N ALA H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.894A pdb=" N TYR H 271 " --> pdb=" O ASP H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 305 removed outlier: 3.503A pdb=" N ARG H 303 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.520A pdb=" N ILE A 138 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN A 12 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 144 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.520A pdb=" N ILE A 138 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN A 12 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR A 5 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 112 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU A 7 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 110 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU A 9 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 108 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE A 102 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 101 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU A 63 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP A 103 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 61 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN A 105 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE A 59 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER A 107 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A 57 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 109 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A 55 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU A 111 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 13.960A pdb=" N VAL A 55 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LEU A 162 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 160 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 228 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 221 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 removed outlier: 5.967A pdb=" N VAL A 24 " --> pdb=" O ALA J 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 218 removed outlier: 6.120A pdb=" N ASP A 214 " --> pdb=" O LEU J 160 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER J 162 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N CYS A 216 " --> pdb=" O SER J 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 246 Processing sheet with id=AA7, first strand: chain 'J' and resid 35 through 37 Processing sheet with id=AA8, first strand: chain 'J' and resid 301 through 305 removed outlier: 3.665A pdb=" N HIS J 304 " --> pdb=" O ILE J 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AB1, first strand: chain 'B' and resid 40 through 42 removed outlier: 3.561A pdb=" N THR B 91 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.006A pdb=" N LEU B 98 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 142 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 19 through 21 Processing sheet with id=AB4, first strand: chain 'I' and resid 25 through 27 Processing sheet with id=AB5, first strand: chain 'I' and resid 25 through 27 removed outlier: 3.815A pdb=" N ILE I 157 " --> pdb=" O LYS I 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 50 through 57 Processing sheet with id=AB7, first strand: chain 'I' and resid 242 through 243 Processing sheet with id=AB8, first strand: chain 'I' and resid 260 through 262 Processing sheet with id=AB9, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.583A pdb=" N ASP D 94 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 31 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.999A pdb=" N ILE D 157 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 160 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 35 current: chain 'E' and resid 158 through 164 Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 90 through 99 current: chain 'E' and resid 242 through 243 Processing sheet with id=AC6, first strand: chain 'E' and resid 50 through 57 Processing sheet with id=AC7, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.614A pdb=" N SER F 20 " --> pdb=" O SER F 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F 108 " --> pdb=" O SER F 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AD1, first strand: chain 'F' and resid 50 through 56 Processing sheet with id=AD2, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AD3, first strand: chain 'G' and resid 106 through 109 removed outlier: 3.733A pdb=" N GLY G 327 " --> pdb=" O PHE G 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 30 through 35 current: chain 'G' and resid 158 through 164 Processing sheet with id=AD5, first strand: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 99 current: chain 'G' and resid 242 through 243 Processing sheet with id=AD6, first strand: chain 'G' and resid 50 through 56 Processing sheet with id=AD7, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.673A pdb=" N SER H 108 " --> pdb=" O SER H 20 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AD9, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE1, first strand: chain 'H' and resid 50 through 57 Processing sheet with id=AE2, first strand: chain 'H' and resid 242 through 243 815 hydrogen bonds defined for protein. 2202 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 7.26 Time building geometry restraints manager: 10.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6902 1.34 - 1.46: 5472 1.46 - 1.58: 12164 1.58 - 1.70: 234 1.70 - 1.82: 193 Bond restraints: 24965 Sorted by residual: bond pdb=" N ASP B 36 " pdb=" CA ASP B 36 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.33e-02 5.65e+03 7.24e+00 bond pdb=" CA PRO H 63 " pdb=" C PRO H 63 " ideal model delta sigma weight residual 1.514 1.522 -0.008 5.50e-03 3.31e+04 2.01e+00 bond pdb=" N LYS B 37 " pdb=" CA LYS B 37 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.77e-02 3.19e+03 1.99e+00 bond pdb=" CA ASP G 51 " pdb=" C ASP G 51 " ideal model delta sigma weight residual 1.528 1.511 0.017 1.33e-02 5.65e+03 1.54e+00 bond pdb=" O5' G C 57 " pdb=" C5' G C 57 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.54e+00 ... (remaining 24960 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.27: 909 105.27 - 112.45: 12641 112.45 - 119.62: 8437 119.62 - 126.80: 11700 126.80 - 133.97: 560 Bond angle restraints: 34247 Sorted by residual: angle pdb=" CA GLU G 278 " pdb=" CB GLU G 278 " pdb=" CG GLU G 278 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CB MET D 229 " pdb=" CG MET D 229 " pdb=" SD MET D 229 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB MET E 328 " pdb=" CG MET E 328 " pdb=" SD MET E 328 " ideal model delta sigma weight residual 112.70 123.57 -10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 123.17 -10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C PRO A 115 " pdb=" N HIS A 116 " pdb=" CA HIS A 116 " ideal model delta sigma weight residual 121.54 128.19 -6.65 1.91e+00 2.74e-01 1.21e+01 ... (remaining 34242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 14095 34.58 - 69.16: 913 69.16 - 103.74: 61 103.74 - 138.32: 0 138.32 - 172.90: 3 Dihedral angle restraints: 15072 sinusoidal: 7168 harmonic: 7904 Sorted by residual: dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual -128.00 44.90 -172.90 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U C 44 " pdb=" C1' U C 44 " pdb=" N1 U C 44 " pdb=" C2 U C 44 " ideal model delta sinusoidal sigma weight residual 232.00 60.18 171.82 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' G C 43 " pdb=" C1' G C 43 " pdb=" N9 G C 43 " pdb=" C4 G C 43 " ideal model delta sinusoidal sigma weight residual 254.00 172.64 81.36 1 1.70e+01 3.46e-03 2.82e+01 ... (remaining 15069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2761 0.038 - 0.077: 774 0.077 - 0.115: 173 0.115 - 0.154: 78 0.154 - 0.192: 10 Chirality restraints: 3796 Sorted by residual: chirality pdb=" C2' U C 1 " pdb=" C3' U C 1 " pdb=" O2' U C 1 " pdb=" C1' U C 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.60 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CB ILE B 102 " pdb=" CA ILE B 102 " pdb=" CG1 ILE B 102 " pdb=" CG2 ILE B 102 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C1' A C 22 " pdb=" O4' A C 22 " pdb=" C2' A C 22 " pdb=" N9 A C 22 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 3793 not shown) Planarity restraints: 3967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG J 188 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C ARG J 188 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG J 188 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU J 189 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 182 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO J 183 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO J 183 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 183 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 328 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C MET E 328 " 0.037 2.00e-02 2.50e+03 pdb=" O MET E 328 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE E 329 " -0.012 2.00e-02 2.50e+03 ... (remaining 3964 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5400 2.78 - 3.31: 21486 3.31 - 3.84: 41441 3.84 - 4.37: 47699 4.37 - 4.90: 81238 Nonbonded interactions: 197264 Sorted by model distance: nonbonded pdb=" O2' G C 11 " pdb=" O PHE H 21 " model vdw 2.252 3.040 nonbonded pdb=" O2' A C 22 " pdb=" O4' U C 23 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP D 94 " pdb=" OG1 THR D 212 " model vdw 2.263 3.040 nonbonded pdb=" O PHE I 21 " pdb=" O2' G C 5 " model vdw 2.270 3.040 nonbonded pdb=" O ALA F 143 " pdb=" OG SER F 174 " model vdw 2.274 3.040 ... (remaining 197259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 12 through 333) selection = (chain 'E' and (resid 12 through 50 or resid 79 through 333)) selection = (chain 'F' and (resid 12 through 50 or resid 79 through 333)) selection = (chain 'G' and (resid 12 through 50 or resid 79 through 333)) selection = (chain 'H' and (resid 12 through 50 or resid 79 through 333)) selection = (chain 'I' and (resid 12 through 50 or resid 79 through 333)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.870 Check model and map are aligned: 0.210 Set scattering table: 0.210 Process input model: 68.010 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24965 Z= 0.169 Angle : 0.597 10.969 34247 Z= 0.318 Chirality : 0.041 0.192 3796 Planarity : 0.004 0.059 3967 Dihedral : 20.198 172.898 9966 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.42 % Allowed : 30.31 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2660 helix: -0.07 (0.18), residues: 762 sheet: 0.63 (0.26), residues: 466 loop : -1.42 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.003 0.001 HIS J 35 PHE 0.013 0.001 PHE I 273 TYR 0.009 0.001 TYR B 96 ARG 0.003 0.000 ARG J 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.9655 (ppp) cc_final: 0.9418 (ppp) REVERT: J 47 ASN cc_start: 0.8739 (m-40) cc_final: 0.8284 (m110) REVERT: J 95 MET cc_start: 0.8344 (mtp) cc_final: 0.7972 (mtp) REVERT: J 97 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6428 (ppp) REVERT: D 221 MET cc_start: 0.8649 (mmm) cc_final: 0.8335 (mmm) REVERT: D 328 MET cc_start: 0.7297 (tmm) cc_final: 0.7019 (ttp) REVERT: E 18 ASN cc_start: 0.8098 (t0) cc_final: 0.7670 (t0) REVERT: E 120 GLN cc_start: 0.8492 (tp40) cc_final: 0.8249 (tp-100) REVERT: H 229 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8202 (tpp) outliers start: 10 outliers final: 3 residues processed: 203 average time/residue: 0.3623 time to fit residues: 117.9163 Evaluate side-chains 141 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain H residue 229 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 185 GLN J 21 ASN J 29 GLN J 213 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 HIS ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 24965 Z= 0.390 Angle : 0.625 9.652 34247 Z= 0.334 Chirality : 0.041 0.247 3796 Planarity : 0.004 0.055 3967 Dihedral : 18.031 172.297 4489 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.22 % Allowed : 28.84 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2660 helix: 0.64 (0.18), residues: 790 sheet: 0.42 (0.27), residues: 440 loop : -1.28 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 149 HIS 0.005 0.001 HIS A 60 PHE 0.018 0.001 PHE J 92 TYR 0.017 0.001 TYR H 114 ARG 0.004 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 135 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 51 ARG cc_start: 0.8650 (ptp-110) cc_final: 0.8292 (tmm-80) REVERT: A 71 ARG cc_start: 0.8034 (mpp80) cc_final: 0.7712 (mpp80) REVERT: J 1 MET cc_start: 0.9621 (ppp) cc_final: 0.9285 (ppp) REVERT: J 68 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7812 (p0) REVERT: J 95 MET cc_start: 0.8657 (mtp) cc_final: 0.8009 (mtt) REVERT: J 116 HIS cc_start: 0.9513 (m90) cc_final: 0.9077 (m-70) REVERT: J 143 THR cc_start: 0.9494 (OUTLIER) cc_final: 0.8959 (t) REVERT: J 322 MET cc_start: 0.9231 (mpp) cc_final: 0.8883 (ttm) REVERT: B 115 MET cc_start: 0.7942 (tmm) cc_final: 0.7672 (tmm) REVERT: D 194 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8459 (tp-100) REVERT: E 18 ASN cc_start: 0.8340 (t0) cc_final: 0.7932 (t0) REVERT: E 120 GLN cc_start: 0.8594 (tp40) cc_final: 0.8389 (tp-100) REVERT: E 325 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.9151 (ttp-170) REVERT: F 229 MET cc_start: 0.8451 (tpp) cc_final: 0.7977 (ttm) REVERT: H 221 MET cc_start: 0.8446 (mmm) cc_final: 0.8196 (mmm) REVERT: H 229 MET cc_start: 0.8937 (tpp) cc_final: 0.8196 (tpp) outliers start: 77 outliers final: 32 residues processed: 202 average time/residue: 0.3816 time to fit residues: 123.9871 Evaluate side-chains 162 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 272 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 251 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 248 optimal weight: 0.0270 chunk 85 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24965 Z= 0.201 Angle : 0.535 11.296 34247 Z= 0.286 Chirality : 0.040 0.260 3796 Planarity : 0.004 0.051 3967 Dihedral : 17.977 171.787 4478 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.76 % Allowed : 28.13 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2660 helix: 0.90 (0.19), residues: 795 sheet: 0.64 (0.28), residues: 402 loop : -1.24 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 149 HIS 0.002 0.001 HIS J 304 PHE 0.019 0.001 PHE J 92 TYR 0.019 0.001 TYR H 114 ARG 0.005 0.000 ARG J 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 140 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8770 (tp) REVERT: J 1 MET cc_start: 0.9615 (ppp) cc_final: 0.9217 (ppp) REVERT: J 95 MET cc_start: 0.8588 (mtp) cc_final: 0.7972 (mtt) REVERT: J 97 MET cc_start: 0.7667 (ppp) cc_final: 0.7388 (ppp) REVERT: J 116 HIS cc_start: 0.9563 (m90) cc_final: 0.9044 (m-70) REVERT: J 143 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9085 (t) REVERT: J 249 CYS cc_start: 0.7829 (t) cc_final: 0.7581 (t) REVERT: J 322 MET cc_start: 0.9294 (mpp) cc_final: 0.9031 (ttm) REVERT: B 104 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5154 (pp20) REVERT: B 115 MET cc_start: 0.7997 (tmm) cc_final: 0.7787 (tmm) REVERT: D 106 MET cc_start: 0.8330 (tmm) cc_final: 0.8012 (tmm) REVERT: D 194 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8417 (tp-100) REVERT: D 221 MET cc_start: 0.8498 (mmm) cc_final: 0.8282 (mmm) REVERT: E 18 ASN cc_start: 0.8253 (t0) cc_final: 0.7835 (t0) REVERT: E 120 GLN cc_start: 0.8589 (tp40) cc_final: 0.8376 (tp-100) REVERT: E 325 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.9133 (ttp-170) REVERT: F 106 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7816 (tmm) REVERT: F 229 MET cc_start: 0.8453 (tpp) cc_final: 0.8022 (ttm) REVERT: F 333 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6232 (mt0) REVERT: H 229 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8261 (tpp) outliers start: 66 outliers final: 35 residues processed: 195 average time/residue: 0.3331 time to fit residues: 105.2382 Evaluate side-chains 173 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 333 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 229 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 0.7980 chunk 188 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 238 optimal weight: 0.0670 chunk 71 optimal weight: 4.9990 overall best weight: 2.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 106 ASN B 120 HIS F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 24965 Z= 0.211 Angle : 0.530 11.729 34247 Z= 0.281 Chirality : 0.040 0.260 3796 Planarity : 0.004 0.051 3967 Dihedral : 17.935 171.264 4478 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.52 % Allowed : 27.00 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2660 helix: 1.07 (0.19), residues: 795 sheet: 0.48 (0.27), residues: 438 loop : -1.14 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 264 HIS 0.006 0.001 HIS A 215 PHE 0.019 0.001 PHE J 92 TYR 0.019 0.001 TYR H 114 ARG 0.003 0.000 ARG J 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 134 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8757 (tp) REVERT: A 14 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: A 71 ARG cc_start: 0.7950 (mpp80) cc_final: 0.7619 (mpp80) REVERT: J 1 MET cc_start: 0.9618 (ppp) cc_final: 0.9208 (ppp) REVERT: J 95 MET cc_start: 0.8616 (mtp) cc_final: 0.8077 (mtt) REVERT: J 97 MET cc_start: 0.7887 (ppp) cc_final: 0.7640 (ppp) REVERT: J 116 HIS cc_start: 0.9632 (m90) cc_final: 0.9207 (m90) REVERT: J 143 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9051 (t) REVERT: J 249 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7576 (t) REVERT: J 322 MET cc_start: 0.9274 (mpp) cc_final: 0.8997 (ttp) REVERT: B 103 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7284 (ttp80) REVERT: B 104 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5405 (pp20) REVERT: B 115 MET cc_start: 0.8055 (tmm) cc_final: 0.7848 (tmm) REVERT: B 123 LEU cc_start: 0.4337 (OUTLIER) cc_final: 0.3775 (pp) REVERT: I 209 ILE cc_start: 0.9150 (pt) cc_final: 0.8881 (mm) REVERT: I 328 MET cc_start: 0.7759 (mtt) cc_final: 0.7458 (mtt) REVERT: D 106 MET cc_start: 0.8341 (tmm) cc_final: 0.8088 (tmm) REVERT: D 194 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8429 (tp-100) REVERT: D 238 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8292 (pttm) REVERT: E 18 ASN cc_start: 0.8263 (t0) cc_final: 0.7851 (t0) REVERT: E 120 GLN cc_start: 0.8591 (tp40) cc_final: 0.8382 (tp-100) REVERT: F 23 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8561 (ptp90) REVERT: F 106 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7691 (tmm) REVERT: F 229 MET cc_start: 0.8477 (tpp) cc_final: 0.8042 (ttm) REVERT: F 253 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8854 (tptp) REVERT: F 333 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6420 (mt0) REVERT: H 229 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8308 (tpp) outliers start: 84 outliers final: 43 residues processed: 205 average time/residue: 0.3520 time to fit residues: 114.4242 Evaluate side-chains 188 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 131 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain J residue 321 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 333 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 309 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 136 optimal weight: 0.0770 chunk 239 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN B 120 HIS I 77 GLN F 77 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 24965 Z= 0.153 Angle : 0.520 12.915 34247 Z= 0.272 Chirality : 0.039 0.260 3796 Planarity : 0.003 0.051 3967 Dihedral : 17.872 170.821 4478 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.89 % Allowed : 27.75 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2660 helix: 1.14 (0.19), residues: 795 sheet: 0.64 (0.27), residues: 428 loop : -1.12 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 264 HIS 0.004 0.000 HIS A 215 PHE 0.019 0.001 PHE J 92 TYR 0.017 0.001 TYR H 114 ARG 0.009 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 140 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8749 (tp) REVERT: A 14 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: A 71 ARG cc_start: 0.7951 (mpp80) cc_final: 0.7571 (mpp80) REVERT: A 140 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8511 (ttm-80) REVERT: A 146 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7861 (mtp-110) REVERT: J 1 MET cc_start: 0.9615 (ppp) cc_final: 0.9214 (ppp) REVERT: J 95 MET cc_start: 0.8686 (mtp) cc_final: 0.8170 (mtt) REVERT: J 97 MET cc_start: 0.8029 (ppp) cc_final: 0.7757 (ppp) REVERT: J 116 HIS cc_start: 0.9649 (m90) cc_final: 0.9153 (m90) REVERT: J 143 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9016 (t) REVERT: J 322 MET cc_start: 0.9260 (mpp) cc_final: 0.9008 (ttp) REVERT: B 103 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7447 (ttp80) REVERT: B 104 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.5480 (pp20) REVERT: B 115 MET cc_start: 0.8036 (tmm) cc_final: 0.7802 (tmm) REVERT: B 123 LEU cc_start: 0.4312 (OUTLIER) cc_final: 0.3764 (pp) REVERT: I 209 ILE cc_start: 0.9155 (pt) cc_final: 0.8870 (mm) REVERT: D 221 MET cc_start: 0.8405 (mmm) cc_final: 0.8104 (mmm) REVERT: D 238 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8301 (pttm) REVERT: E 18 ASN cc_start: 0.8233 (t0) cc_final: 0.7834 (t0) REVERT: E 120 GLN cc_start: 0.8605 (tp40) cc_final: 0.8356 (tp-100) REVERT: F 23 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8508 (ptp90) REVERT: F 106 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7734 (tmm) REVERT: F 229 MET cc_start: 0.8458 (tpp) cc_final: 0.8023 (ttm) REVERT: F 333 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6322 (mt0) REVERT: H 106 MET cc_start: 0.8178 (tmm) cc_final: 0.7934 (tmm) REVERT: H 229 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8265 (tpp) outliers start: 69 outliers final: 40 residues processed: 196 average time/residue: 0.3446 time to fit residues: 109.1022 Evaluate side-chains 182 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 131 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 333 GLN Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 229 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 120 HIS B 130 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 24965 Z= 0.328 Angle : 0.590 13.914 34247 Z= 0.306 Chirality : 0.041 0.330 3796 Planarity : 0.004 0.054 3967 Dihedral : 17.915 170.727 4478 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.10 % Allowed : 27.50 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2660 helix: 1.11 (0.19), residues: 798 sheet: 0.44 (0.26), residues: 438 loop : -1.10 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 264 HIS 0.005 0.001 HIS A 215 PHE 0.018 0.001 PHE J 92 TYR 0.019 0.001 TYR A 142 ARG 0.005 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 133 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8712 (tp) REVERT: A 14 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: J 1 MET cc_start: 0.9614 (ppp) cc_final: 0.9220 (ppp) REVERT: J 95 MET cc_start: 0.8710 (mtp) cc_final: 0.8130 (mtt) REVERT: J 116 HIS cc_start: 0.9677 (m90) cc_final: 0.9229 (m90) REVERT: J 143 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9024 (t) REVERT: J 322 MET cc_start: 0.9278 (mpp) cc_final: 0.8983 (ttp) REVERT: B 103 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7398 (ttp80) REVERT: B 104 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.5913 (pp20) REVERT: B 115 MET cc_start: 0.8076 (tmm) cc_final: 0.7826 (tmm) REVERT: B 123 LEU cc_start: 0.4759 (OUTLIER) cc_final: 0.4196 (pp) REVERT: I 209 ILE cc_start: 0.9200 (pt) cc_final: 0.8800 (mm) REVERT: D 194 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8568 (tp-100) REVERT: D 238 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8305 (pttm) REVERT: E 18 ASN cc_start: 0.8275 (t0) cc_final: 0.7879 (t0) REVERT: E 120 GLN cc_start: 0.8568 (tp40) cc_final: 0.8349 (tp-100) REVERT: F 106 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7759 (tmm) REVERT: F 229 MET cc_start: 0.8514 (tpp) cc_final: 0.8033 (ttm) REVERT: F 328 MET cc_start: 0.8048 (tmm) cc_final: 0.7772 (tmm) REVERT: F 333 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6530 (mt0) REVERT: G 229 MET cc_start: 0.8558 (tpp) cc_final: 0.8334 (tpp) REVERT: H 229 MET cc_start: 0.8965 (tpp) cc_final: 0.8337 (tpp) outliers start: 74 outliers final: 50 residues processed: 195 average time/residue: 0.3598 time to fit residues: 112.8818 Evaluate side-chains 187 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 127 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain J residue 321 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 333 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 309 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 152 optimal weight: 0.0040 chunk 195 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS F 77 GLN F 120 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24965 Z= 0.140 Angle : 0.549 14.104 34247 Z= 0.281 Chirality : 0.039 0.266 3796 Planarity : 0.003 0.052 3967 Dihedral : 17.922 170.182 4477 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.13 % Allowed : 28.09 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2660 helix: 1.21 (0.19), residues: 801 sheet: 0.64 (0.26), residues: 433 loop : -1.07 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 33 HIS 0.003 0.000 HIS A 215 PHE 0.019 0.001 PHE J 92 TYR 0.014 0.001 TYR A 142 ARG 0.005 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 139 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8701 (tp) REVERT: A 14 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: A 71 ARG cc_start: 0.8036 (mpp80) cc_final: 0.7735 (mpp80) REVERT: J 1 MET cc_start: 0.9609 (ppp) cc_final: 0.9223 (ppp) REVERT: J 95 MET cc_start: 0.8751 (mtp) cc_final: 0.8205 (mtt) REVERT: J 116 HIS cc_start: 0.9676 (m90) cc_final: 0.9176 (m90) REVERT: J 143 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9027 (t) REVERT: J 322 MET cc_start: 0.9256 (mpp) cc_final: 0.8966 (ttp) REVERT: B 104 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.5619 (pp20) REVERT: B 115 MET cc_start: 0.8010 (tmm) cc_final: 0.7786 (tmm) REVERT: B 123 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4077 (pp) REVERT: I 209 ILE cc_start: 0.9168 (pt) cc_final: 0.8864 (mm) REVERT: D 221 MET cc_start: 0.8397 (mmm) cc_final: 0.8059 (mmm) REVERT: D 238 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8277 (pttm) REVERT: E 18 ASN cc_start: 0.8144 (t0) cc_final: 0.7720 (t0) REVERT: E 120 GLN cc_start: 0.8545 (tp40) cc_final: 0.8221 (tp-100) REVERT: F 106 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7810 (tmm) REVERT: F 328 MET cc_start: 0.7971 (tmm) cc_final: 0.7697 (tmm) REVERT: H 229 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8297 (tpp) outliers start: 51 outliers final: 31 residues processed: 178 average time/residue: 0.3368 time to fit residues: 96.8225 Evaluate side-chains 168 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 229 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 169 optimal weight: 0.4980 chunk 181 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 24 optimal weight: 0.0670 chunk 209 optimal weight: 10.0000 overall best weight: 4.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN B 120 HIS F 77 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24965 Z= 0.272 Angle : 0.588 13.646 34247 Z= 0.301 Chirality : 0.040 0.276 3796 Planarity : 0.004 0.053 3967 Dihedral : 17.951 170.493 4477 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.60 % Allowed : 28.00 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2660 helix: 1.21 (0.19), residues: 797 sheet: 0.58 (0.26), residues: 433 loop : -1.06 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 264 HIS 0.003 0.001 HIS A 215 PHE 0.016 0.001 PHE J 92 TYR 0.017 0.001 TYR A 142 ARG 0.006 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 129 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8699 (tp) REVERT: A 14 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: A 71 ARG cc_start: 0.8012 (mpp80) cc_final: 0.7652 (mpp80) REVERT: J 1 MET cc_start: 0.9615 (ppp) cc_final: 0.9309 (ppp) REVERT: J 95 MET cc_start: 0.8827 (mtp) cc_final: 0.8295 (mtt) REVERT: J 116 HIS cc_start: 0.9681 (m90) cc_final: 0.9236 (m90) REVERT: J 123 ASP cc_start: 0.9131 (p0) cc_final: 0.8754 (p0) REVERT: J 143 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.9015 (t) REVERT: J 322 MET cc_start: 0.9263 (mpp) cc_final: 0.8957 (ttp) REVERT: B 104 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6105 (pp20) REVERT: B 115 MET cc_start: 0.8036 (tmm) cc_final: 0.7785 (tmm) REVERT: B 123 LEU cc_start: 0.4965 (OUTLIER) cc_final: 0.4392 (pp) REVERT: I 209 ILE cc_start: 0.9195 (pt) cc_final: 0.8793 (mm) REVERT: D 221 MET cc_start: 0.8481 (mmm) cc_final: 0.8094 (mmm) REVERT: D 238 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8328 (pttm) REVERT: E 18 ASN cc_start: 0.8197 (t0) cc_final: 0.7785 (t0) REVERT: E 120 GLN cc_start: 0.8542 (tp40) cc_final: 0.8304 (tp-100) REVERT: F 106 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7776 (tmm) REVERT: F 249 MET cc_start: 0.8018 (tpp) cc_final: 0.7814 (mtp) REVERT: F 328 MET cc_start: 0.8033 (tmm) cc_final: 0.7777 (tmm) REVERT: G 229 MET cc_start: 0.8546 (tpp) cc_final: 0.8330 (tpp) REVERT: H 229 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8340 (tpp) REVERT: H 284 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8454 (mtm110) outliers start: 62 outliers final: 44 residues processed: 180 average time/residue: 0.3316 time to fit residues: 96.3585 Evaluate side-chains 181 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 284 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24965 Z= 0.215 Angle : 0.576 14.306 34247 Z= 0.295 Chirality : 0.040 0.260 3796 Planarity : 0.004 0.052 3967 Dihedral : 17.962 170.212 4477 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.34 % Allowed : 28.34 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2660 helix: 1.18 (0.19), residues: 800 sheet: 0.49 (0.26), residues: 443 loop : -1.04 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 264 HIS 0.003 0.001 HIS G 60 PHE 0.016 0.001 PHE J 92 TYR 0.013 0.001 TYR H 114 ARG 0.007 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 129 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8706 (tp) REVERT: A 14 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: A 71 ARG cc_start: 0.8040 (mpp80) cc_final: 0.7678 (mpp80) REVERT: A 140 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8354 (ttm-80) REVERT: J 1 MET cc_start: 0.9614 (ppp) cc_final: 0.9339 (ppp) REVERT: J 95 MET cc_start: 0.8837 (mtp) cc_final: 0.8427 (mtt) REVERT: J 116 HIS cc_start: 0.9678 (m90) cc_final: 0.9218 (m90) REVERT: J 123 ASP cc_start: 0.9113 (p0) cc_final: 0.8890 (p0) REVERT: J 143 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9022 (t) REVERT: J 322 MET cc_start: 0.9257 (mpp) cc_final: 0.8969 (ttm) REVERT: B 104 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6089 (pp20) REVERT: B 115 MET cc_start: 0.8016 (tmm) cc_final: 0.7782 (tmm) REVERT: B 123 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4437 (pp) REVERT: I 209 ILE cc_start: 0.9201 (pt) cc_final: 0.8826 (mm) REVERT: D 194 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8497 (tp-100) REVERT: D 221 MET cc_start: 0.8493 (mmm) cc_final: 0.8077 (mmm) REVERT: D 238 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8303 (pttm) REVERT: E 18 ASN cc_start: 0.8163 (t0) cc_final: 0.7736 (t0) REVERT: E 120 GLN cc_start: 0.8527 (tp40) cc_final: 0.8252 (tp-100) REVERT: F 106 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7824 (tmm) REVERT: G 229 MET cc_start: 0.8532 (tpp) cc_final: 0.8310 (tpp) REVERT: H 229 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8335 (tpp) outliers start: 56 outliers final: 42 residues processed: 174 average time/residue: 0.3427 time to fit residues: 97.9656 Evaluate side-chains 177 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 126 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain J residue 321 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 219 CYS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 124 optimal weight: 0.0670 chunk 182 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24965 Z= 0.226 Angle : 0.582 14.366 34247 Z= 0.297 Chirality : 0.040 0.256 3796 Planarity : 0.004 0.051 3967 Dihedral : 17.962 170.191 4477 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.34 % Allowed : 28.21 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2660 helix: 1.20 (0.19), residues: 799 sheet: 0.57 (0.26), residues: 433 loop : -1.06 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 264 HIS 0.003 0.001 HIS A 215 PHE 0.015 0.001 PHE J 92 TYR 0.016 0.001 TYR I 210 ARG 0.009 0.000 ARG A 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 129 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8705 (tp) REVERT: A 14 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: A 71 ARG cc_start: 0.8064 (mpp80) cc_final: 0.7679 (mpp80) REVERT: A 140 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8329 (ttm-80) REVERT: J 1 MET cc_start: 0.9611 (ppp) cc_final: 0.9410 (ppp) REVERT: J 95 MET cc_start: 0.8857 (mtp) cc_final: 0.8449 (mtt) REVERT: J 116 HIS cc_start: 0.9676 (m90) cc_final: 0.9260 (m90) REVERT: J 123 ASP cc_start: 0.9122 (p0) cc_final: 0.8896 (p0) REVERT: J 143 THR cc_start: 0.9508 (OUTLIER) cc_final: 0.9022 (t) REVERT: J 322 MET cc_start: 0.9257 (mpp) cc_final: 0.8949 (ttp) REVERT: B 104 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6259 (pp20) REVERT: B 115 MET cc_start: 0.8027 (tmm) cc_final: 0.7784 (tmm) REVERT: B 123 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4508 (pp) REVERT: I 209 ILE cc_start: 0.9218 (pt) cc_final: 0.8835 (mm) REVERT: D 194 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8529 (tp-100) REVERT: D 221 MET cc_start: 0.8490 (mmm) cc_final: 0.8214 (mmm) REVERT: D 238 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8328 (pttm) REVERT: E 18 ASN cc_start: 0.8169 (t0) cc_final: 0.7739 (t0) REVERT: E 120 GLN cc_start: 0.8524 (tp40) cc_final: 0.8268 (tp-100) REVERT: F 106 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7776 (tmm) REVERT: H 229 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8392 (tpp) outliers start: 56 outliers final: 47 residues processed: 175 average time/residue: 0.3405 time to fit residues: 99.1940 Evaluate side-chains 184 residues out of total 2390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 128 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 200 SER Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 286 GLN Chi-restraints excluded: chain J residue 321 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 192 optimal weight: 0.0010 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.042065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.029688 restraints weight = 133383.716| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 4.06 r_work: 0.2435 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24965 Z= 0.183 Angle : 0.567 14.961 34247 Z= 0.289 Chirality : 0.039 0.254 3796 Planarity : 0.003 0.052 3967 Dihedral : 17.965 170.047 4477 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.51 % Allowed : 28.09 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2660 helix: 1.24 (0.19), residues: 800 sheet: 0.60 (0.26), residues: 433 loop : -1.02 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 264 HIS 0.003 0.000 HIS A 215 PHE 0.017 0.001 PHE J 92 TYR 0.017 0.001 TYR I 210 ARG 0.010 0.000 ARG A 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4339.23 seconds wall clock time: 83 minutes 56.11 seconds (5036.11 seconds total)